/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks31-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks32-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks33-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks34-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks35-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Dendrolagus_matschiei-Dendrolagus_matschiei_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks31-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks32-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks33-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Macropus_rufogriseus-Macropus_rufogriseus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks10.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks11.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks12.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks13.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks14.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks15.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks16.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks17.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks18.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks19.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks1.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks20.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks21.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks22.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks23.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks2.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks3.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks4.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks5.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks6.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks7.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks8.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Eulemur_macaco-Eulemur_macaco_HiC/chunks9.fa --ambiguous=iupac --format=maf > Eulemur_macaco-Eulemur_macaco_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9.fa --ambiguous=iupac --format=maf > Miopithecus_talapoin-Miopithecus_talapoin_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Trachypithecus_obscurus-Trachypithecus_obscurus_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr8.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr16.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr1.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr17.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr17.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr8.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr15.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr17.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr8.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr14.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr8.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chrM.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chrM.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr16.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr20.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-mm10-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr8.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programformat=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cer2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanforcopithecus_mitis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundajd/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbe/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=ielli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hgercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marino38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1vg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithe9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --cus_campbelli_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_caambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.mpbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_Hilastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbellC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_i_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunmitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/pks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-rograms/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cchr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguousercopithecus_mitis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecu=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrs_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/aku7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr12.maf
/oak/sndaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maftanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-C=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopiercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrthecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/a17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-kundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopith32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanfecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbord/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinoM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_vg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cmitis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopiercopithecus_campbelli_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopitthecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --forhecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/mat=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/clastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_camhunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopipbelli_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrY.maf
thecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr6.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr6.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr12.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr14.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr20.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Chlorocebus_pygerythrus-Chlorocebus_pygerythrus_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Allochrocebus_lhoesti-Allochrocebus_lhoesti_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_campbelli-Cercopithecus_campbelli_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_mitis-Cercopithecus_mitis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-hg38-chr4.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr12.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr2.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr15.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-hg38-chr20.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks16-vs-mm10-chrM.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-hg38-chr1.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks20-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-hg38-chrX.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-hg38-chr6.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr14.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr17.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-hg38-chr3.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks5-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr17.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-hg38-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_nictitans-Cercopithecus_nictitans_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cercopithecus_pogonias-Cercopithecus_pogonias_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks10.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks1.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks2.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks3.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks4.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks5.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks6.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks7.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks8.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --amb/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks10.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks11.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks12.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks13.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks14.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks15.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks16.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks17.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks18.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks19.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks1.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks20.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks21.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks22.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks2.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks3.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks4.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks5.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks6.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks7.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks8.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Papio_papio-Papio_papio_HiC/chunks9.fa --ambiguous=iupac --format=maf > Papio_papio-Papio_papio_HiC/chunks9-vs-mm10-chrY.maf
iguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Cricetulus_griseus-CriGri-PICR_HiC/chunks9.fa --ambiguous=iupac --format=maf > Cricetulus_griseus-CriGri-PICR_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mesocricetus_auratus-golden_hamster_wtdbg2.shortReadsPolished_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Xerus_rutilus-Xerus_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Xerus_rutilus-Xerus_rutilus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks21.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks22.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks23.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_libycus-Meriones_libycusi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_libycus-Meriones_libycusi_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-ASM813125v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-ASM813125v1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Meriones_unguiculatus-GCA_008131255.1_ASM813125v1_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_agrestis-GCA_001305995.1_ASM130599v1_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_mexicanus-Microtus_mexicanus_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Microtus_oregoni-GCA_018167655.1_Mior012_genomic_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sigmodon_hispidus-GCA_004025045.1_SigHis_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_crinitus-pecr10X_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_crinitus-pecr10X_v2_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks31-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks32-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks33-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks34-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_difficilis-Peromyscus_difficilis_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks21.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks22.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks23.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks24.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_eremicus-Peer1.6.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_eremicus-Peer1.6.0_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Peromyscus_nasutus-Peromyscus_nasutus_10x_v1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_forsteri-Arctocephalus_forsteri_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9.fa --ambiguous=iupac --format=maf > Arctocephalus_townsendi-Arctocephalus_townsendi_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-GCA_014825515.1_WHU_Ajam_v2_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9.fa --ambiguous=iupac --format=maf > Artibeus_jamaicensis-WHU_Ajam_v2_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Balaenoptera_borealis-Balaenoptera_borealis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_astutus-Bassariscus_astutus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9.fa --ambiguous=iupac --format=maf > Bassariscus_sumichrasti-Bassariscus_sumichrasti_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9.fa --ambiguous=iupac --format=maf > Carollia_perspicillata-CarPer_v1_BIUU_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks10.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks11.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks12.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks13.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks14.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks15.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks16.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks17.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks1.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks2.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks3.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks4.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks5.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks6.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks7.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks8.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Felis_nigripes-Felis_nigripes_HiC/chunks9.fa --ambiguous=iupac --format=maf > Felis_nigripes-Felis_nigripes_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Lasiurus_seminolus-Lasiurus_seminolus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Leopardus_tigrinus-Leopardus_tigrinus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Martes_flavigula-mfla.min_150.pseudohap2.1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_muntjak-CMJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_muntjak-CMJ_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks10.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks11.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks12.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks13.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks14.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks15.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks16.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks17.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks1.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks2.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks3.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks4.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks5.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks6.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks7.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks8.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Muntiacus_reevesi-CIJ_HiC/chunks9.fa --ambiguous=iupac --format=maf > Muntiacus_reevesi-CIJ_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_erminea-Mustela_erminea_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_erminea-Mustela_erminea_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nigripes-musNig1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nigripes-musNig1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks25.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Mustela_nivalis-Mustela_nivalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Mustela_nivalis-Mustela_nivalis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks24.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks25.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks26.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks27.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks28.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myodes_rutilus-Myodes_rutilus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myodes_rutilus-Myodes_rutilus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_lucifugus-Myoluc2.0_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_lucifugus-Myoluc2.0_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks4-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr13.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr15.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks8-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr12.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr21.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr5.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_septentrionalis-myse_ont_racon_pilon_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Myotis_yumanensis-Myotis_yumanensis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks10.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks11.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks12.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks13.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks14.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks15.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks16.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks17.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks18.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks19.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks1.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks20.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks21.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks22.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks23.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks24.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks25.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks26.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks27.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks27-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks28.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks28-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks29.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks29-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks2.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks30.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks30-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks3.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks4.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks5.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks6.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks7.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks8.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Neotoma_phenax-Neotoma_phenax_HiC/chunks9.fa --ambiguous=iupac --format=maf > Neotoma_phenax-Neotoma_phenax_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Onychomys_leucogaster-Onychomys_leucogaster_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks10.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks11.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks12.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks13.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks14.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks15.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks16.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks17.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks18.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks19.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks1.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks20.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks21.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks2.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks3.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks4.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks5.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks6.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks7.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks8.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Oryx_dammah-oryx.1_HiC/chunks9.fa --ambiguous=iupac --format=maf > Oryx_dammah-oryx.1_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9.fa --ambiguous=iupac --format=maf > Ovis_canadensis-GCA_004026945.1_OviCan_v1_BIUU_genomic_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9.fa --ambiguous=iupac --format=maf > Prionailurus_viverrinus-Prionailurus_viverrinus_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks25-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks26-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9.fa --ambiguous=iupac --format=maf > Romerolagus_diazi-Romerolagus_diazi_prelim_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9.fa --ambiguous=iupac --format=maf > Sylvilagus_transitionalis-Sylvilagus_transitionalis_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks1-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks21-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks22-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks23-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks24-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks2-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks4-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9.fa --ambiguous=iupac --format=maf > Tapirus_terrestris-Tapirus_terrestris_HiC/chunks9-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-hg38-chr19.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr12.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks10-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks11-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks12-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks13-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks14-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-hg38-chr1.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks15-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-hg38-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks16-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks17-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks18-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks19-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-hg38-chr20.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr18.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks1-vs-mm10-chr7.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks20-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr1.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chr4.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks21-vs-mm10-chrY.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr1.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-hg38-chr4.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr10.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr12.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks2-vs-mm10-chr9.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks3-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks4-vs-hg38-chr20.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks5-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks6-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks7-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr22.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrX.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks8-vs-mm10-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr20.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr20.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr21.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr21.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chr22.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chr22.maf
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/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 hg38-chrY.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-hg38-chrY.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr10.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr10.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr11.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr11.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr12.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr12.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr13.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr13.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr14.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr14.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr15.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr15.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr16.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr16.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr17.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr17.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr18.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr18.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr19.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr19.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr1.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr1.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr2.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr2.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr3.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr3.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr4.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr4.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr5.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr5.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr6.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr6.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr7.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr7.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr8.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr8.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chr9.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chr9.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrM.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chrM.maf
/oak/stanford/groups/akundaje/marinovg/programs/lastz-1.04.00-32/bin/lastz_32 mm10-chrX.fa Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9.fa --ambiguous=iupac --format=maf > Urocyon_littoralis_catalinae-Urocyon_littoralis_catalinaei_HiC/chunks9-vs-mm10-chrX.maf
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